*/Disease Information(sort of like the Intro to your MiniResearch Writeup): Plasmodium berghei is a type of bacteria that can be found to cause malaria in mice. The malaria bacteria is transmitted through female mosquito bites, and the bacteria travels to the liver for reproduction. After a short while, the bacteria then leaves the liver and invades red blood cells that go through the circulatory system. Side effects include anemia and damage to essential host organs, but one side effect found mostly in mice is the cerebral complications.
Expression Information (has it been expressed in bacterial cells): Brenda has no expression in things other than homo sapiens, but the PDB article cited below has an expression in E. coli.
*length of your protein in Amino Acids 132 Amino Acids
Molecular Weightof your protein in kiloDaltons using theExpasy ProtParamwebsite 15.3357 kDa
Molar Extinction coefficientof your protein at 280 nm wavelength: Expasy ProtParam detected no TRP residues so there can be greater than 10% error. But the extinction coefficient measured at 280 nm in water was 11920 1/M*cm.
*NCBI Gene # or RefSeq#: NCBIGene ID: 3428686 PB000903.02.0
*Protein ID (NP or XP #) or Wolbachia#: XP_680051.1
*Organism (including strain): Plasmodium berghei strain ANKA
Etiologic Risk Group (see link below): Risk Group 2
http://osp.od.nih.gov/sites/default/files/NIH_Guidelines.html
*/Disease Information(sort of like the Intro to your MiniResearch Writeup): Plasmodium berghei is a type of bacteria that can be found to cause malaria in mice. The malaria bacteria is transmitted through female mosquito bites, and the bacteria travels to the liver for reproduction. After a short while, the bacteria then leaves the liver and invades red blood cells that go through the circulatory system. Side effects include anemia and damage to essential host organs, but one side effect found mostly in mice is the cerebral complications.
Link to TDR Targets page (if present): N/A
Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.) http://www.ncbi.nlm.nih.gov/gene/3428686
Essentiality of this protein: http://www.pnas.org/content/93/23/13143.full.pdf http://mcb.asm.org/content/27/13/4784.short
Histone deacetylase is essential in transcription of eukaryotic DNA by removing acetyl groups from histones.
Is it a monomer or multimer as biological unit? (make prediction at http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html): Monomeric
Complex of proteins?: No. One protein. 3 amino acids and 12 ligands in ASU
Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism): Apicidin
http://www.pnas.org/content/93/23/13143.full.pdf
*EC#: 3.5.1.98
Link to BRENDA EC# page: http://www.brenda-enzymes.org/enzyme.php?ecno=3.5.1.98
-- Show screenshot of BRENDA enzyme mechanism schematic
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):
Fluor de Lys kit from BioMol.
Uses fluorescence
Reagent: acetylated lysine side chains, nuclear or cellular extract
-- link to Sigma (or othercompany) page for assay (see Sigma links below)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2431080/
-- -or link (or citation) to paper that contains assay information
-- links to assay reagents (substrates) pages.
http://www.enzolifesciences.com/BML-KI104/fluor-de-lys-deacetylase-substrate/
--- List cost and quantity of substrate reagents, supplier, and catalog #
Structure (PDB or Homology model)
-- PDB # or closest PDB entry if using homology model: PDB: 3C0Y
-- For Homology Model option: N/A
---- Show pairwise alignment of your BLASTP search in NCBI against the PDB
---- Query Coverage:
---- Max % Identities:
---- % Positives
---- Chain used for homology:
Current Inhibitors:
Apicidin
http://www.jstor.org/stable/40761?seq=1#page_scan_tab_contents
Expression Information (has it been expressed in bacterial cells):
Brenda has no expression in things other than homo sapiens, but the PDB article cited below has an expression in E. coli.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2431080/
Purification Method: Purification of homogeneity by anion-exchange chromatography after dilution with buffer.
Image of protein (PyMol with features delineated and shown separately):
*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
VVLNKHHEMS DQISLNDYYD YYAPDFQLHL QPSSIPNYNS PEHLSKIKMK 60 70 80 90 100 ITENLRNIEH APGVQFSYVP PDFFDSDIDD KSDKNQYELK DDSGGGRAAG 110 120 130 TRGKEHSSTH HLRRKNYEDD FFDMSDRDQG II*length of your protein in Amino Acids132 Amino Acids
Molecular Weight of your protein in kiloDaltons using theExpasy ProtParamwebsite
15.3357 kDa
Molar Extinction coefficient of your protein at 280 nm wavelength:
Expasy ProtParam detected no TRP residues so there can be greater than 10% error.
But the extinction coefficient measured at 280 nm in water was 11920 1/M*cm.
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
*CDSGene Sequence(paste as text only):
gtggtgctgaacaaacatcatgaaatgagcgatcagattagcctgaacgattattatgat tattatgcgccggattttcagctgcatctgcagccgagcagcattccgaactataacagc ccggaacatctgagcaaaattaaaatgaaaattaccgaaaacctgcgcaacattgaacat gcgccgggcgtgcagtttagctatgtgccgccggatttttttgatagcgatattgatgat aaaagcgataaaaaccagtatgaactgaaagatgatagcggcggcggccgcgcggcgggc acccgcggcaaagaacatagcagcacccatcatctgcgccgcaaaaactatgaagatgat ttttttgatatgagcgatcgcgatcagggcattatt
*GC% Content for gene: 46.2%
*CDS Gene Sequence (codon optimized) - copy fromoutputofPrimer DesignProtocol (paste as text only):
*GC% Content for gene (codon optimized):
Told not to do until the target was selected.
Do Not Need this info for Spring (but still copy these lines to your Target page for now)
Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):
(link to DNA Works outputtext file-that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences):
**